Workflow

human_genomics_pipeline processes paired-end sequencing data (WGS or WES) using bwa, sambamba and GATK4. It is based on the GATK4 best practices for data pre-processing for variant discovery

Run parameters:
  • Input data type: Single
  • Reference genome: /store/lkemp/publicData/referenceGenome/gatkBundle/GRCh37/ucsc.hg19.fasta
  • dbSNP database /store/lkemp/publicData/dbSNP/gatkBundle/GRCh37/dbsnp_138.hg19.vcf

Click the nodes to obtain details about each step.

Base recalibration

Quality checks

Trimming

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

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